[Funcoup] Featured Article

Erik Sonnhammer Erik.Sonnhammer at sbc.su.se
Tue Nov 29 16:27:34 CET 2011


Hi, I'm a bit sceptical to using 'robust', given the huge differences 
between fc1 and fc2.  It would need to be qualified and that will be 
hard in a lay summary.

/Erik

On 11/29/2011 02:53 PM, Andrey Alexeyenko wrote:
>> The problem with "largest reconstruction of gene networks to date" is
>> that STRING has 1000 species and is surely a lot larger (in total).
> Hence I suggest "ROBUST  ... owing to ... orthologs AND SUPERVISED LEARNING"
>> The FunCoup 2.0 database provides the largest gene network
>> reconstructions to date for 11 eukaryotes, ..."
>>
>> But really to say this we should check if this is true for all 11
>> species. Aside from STRING there are a bunch of other databases
>> (referenced in our paper).  Any volunteers?
> As soon as there is no DB with>10 species of comparable size, one can
> say "the largest reconstruction " - the latter term refers to the whole
> thing...
>
> A
>
>>
>> /Erik
>>
>> On 11/29/2011 02:07 PM, Andrey Alexeyenko wrote:
>>> Hi,
>>>
>>> I suggest the most parsimonious (and least humble) edit:
>>> "provides the largest ROBUST reconstruction of gene networks to date,
>>> owing to the extensive transfer of evidence between species via
>>> orthologs AND SUPERVISED LEARNING ON SPECIES OWN DATA"
>>>
>>> This recognizes advantage compared to STRING. But if there is another
>>> database with more than ~50 million links in more that 10 eukaryotic
>>> species that uses orthologs and KEGG-based training sets, then it's
>>> wrong, and I'd agree with Erik's version.
>>>
>>> Andrey
>>>
>>> On 2011-11-29 13:31, Erik Sonnhammer wrote:
>>>> Hi, this is a nice surprise, see below.
>>>>
>>>> But personally I find their lay summary it a bit too boasting, given
>>>> that we only cover 11 species.
>>>>
>>>> how about
>>>>
>>>> The FunCoup 2.0 database provides very comprehensive reconstructions of
>>>> gene networks, owing to the extensive transfer of evidence between
>>>> species via orthologs, and Bayesian integration of nine different data
>>>> source types. The FunCoup website allows local network alignment between
>>>> multiple species.
>>>>
>>>> instead?
>>>>
>>>> /Erik
>>>>
>>>> -------- Original Message --------
>>>> Subject: Nucleic Acids Research - NAR-02446-DATA-E-2011.R1
>>>> Date: Tue, 29 Nov 2011 06:20:53 -0500 (EST)
>>>> From: nar at soton.ac.uk
>>>> To: erik.sonnhammer at sbc.su.se
>>>>
>>>> 29-Nov-2011
>>>>
>>>> NAR-02446-DATA-E-2011.R1 - Comparative interactomics with Funcoup 2.0
>>>>
>>>> Dear Prof. Sonnhammer:
>>>>
>>>> I am pleased to inform you that your article has been chosen by the
>>>> Editors of Nucleic Acids Research to appear on our Featured Articles
>>>> page
>>>> (http://www.oxfordjournals.org/our_journals/nar/featured_articles.html).
>>>> Featured Articles represent the top 5% of NAR papers in terms of
>>>> originality, significance and scientific excellence.
>>>>
>>>> Each article appearing on this page is accompanied by a short Lay
>>>> Summary. The Lay Summary for your article is added below for your
>>>> information. If you wish to make corrections to the Summary, please
>>>> email me within 48h of this email (nar at soton.ac.uk). Please note that
>>>> your Summary should be no longer than 100 words and only minor
>>>> corrections are allowed at this stage.
>>>>
>>>> Lay Summary:
>>>> The FunCoup 2.0 database provides the largest reconstruction of gene
>>>> networks to date, owing to the extensive transfer of evidence between
>>>> species via orthologs and Bayesian integration of nine different data
>>>> source types. The FunCoup website allows local network alignment between
>>>> multiple species.
>>>>
>>>> With best wishes
>>>>
>>>> Martine Bernardes Silva
>>>>
>>>> Nucleic Acids Research
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